How can I explore tSNE/UMAP plots?
One of the goals of exploring a tSNE/UMAP map (as with any other dimensionality-reduced datasets) is to characterize the populations defined by it. In cytometry, this means defining the phenotypes of populations/”islands” defined on the plots to give them biologically-relevant naming. FCS Express allows users to efficiently explore and name populations in multiple ways: classical backgating, parameter overlays and density plots.
One of the most important steps in high-dimensional data analysis is the exploration of the dimensionality-reduced dataset obtained after tSNE, UMAP or other dimensionality-reduction algorithms. One of the aims of this step is the biological classification of the different populations mapped on the map. In FCS Express this process is extremely easy and dynamic.
Some options and ideas for visualization and analysis are presented below.
After creating a gate around population of interest on the dimensionality-reduced dataset (e.g. tSNE map, UMAP map, PCA, map,...) the population of interest can be backgated on classical 2D Color Dot Plots.
The gate of interest can then be moved around on the map allowing you to immediately see the population of interest backgated on Color Dot plots which will update in real time.
Tip 1: the NxN Multiplots feature can be used to quickly create an NxN matrix of plots.
Tip 2: the population of interest can be emphasized to make its identification easier on Color Dot Plots which is especially useful when the population is rare.
The phenotype of a population of interest can also be investigated using Parameter Overlays. The parameter overlay feature allows users to plot the distribution of the parameters on an overlaid histogram (a separate overlay for each parameter) that may be gated on population of interest defined on the map. By utilizing parameter overlays users can quickly assess the distribution of many markers across many parameters within a gated population.
Tip: Overlay can be easily customized via the Overlay Formatting dialog.
Event on Density Plots are usually colored based on the density distribution of cells within the plot itself (counts). The density heat mapping can also be representative of the heat of any parameter in the data set. For example, events on a density plot can be colored based on the expression level of a marker/parameter of interest and by visualizing many density plots representing many parameters, researchers can gain insights on which "islands" contain phenotypes of interest and monitor changes between groups.
FCS Express allows users to quickly and easily create and define groups of density plots that will heat map parameters of interest manually on one or few density plots or automatically via the NxN Color by All option.
- Can I get more information regarding the Add-Ons that can be purchased with a license?
- Can I lock my template based on an electronic signature?
- Does FCS Express have any features to help meet 21 CFR Part 11 compliance?
- Does FCS Express have Quality Control features?
- Does FCS Express offer Single Sign On capability?
- How do I configure SQL Server to host a database for FCS Express?
- What database options are available when I purchase the Security option?
- What is the difference between the different types of Users that are available with a Security and Logging license?
- What is the difference between the Logging option and System Level Audit Trails?
- What SQL Server permissions are needed?
- Can I track usage of the internet dongle?
- Can I try out the Internet Dongle before I make a purchase?
- Can the administrator log users out?
- Do you have to be connected to the internet at all times with the Internet dongle?
- How can users be added to an internet dongle license?
- How do I activate my dongle?
- How do I change my internet dongle/site license password?
- How many people can be logged in at the same time?
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- If a user left the computer running can the user log themselves out from another computer?
- What are the differences between the internet dongle and network licensing options?
- What happens if I lose my internet connection?
- What happens if the user leaves the computer without logging out?
- What happens to the users login in case of an unexpected interruption? For instance, a software crash, power failure, etc.
- Why am I receiving a message that FCS Express cannot connect to De Novo Software servers?
- Can I mix Flow, Image, and Plus site licenses? Can I mix site licenses with and without add-ons?
- How are site licenses billed?
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- Can I convert my Cytek license from the countercode licensing option to another licensing option?
- How can I claim my license purchased through BD Accuri Cytometers?
- How can I claim my license purchased through BD Biosciences?
- How can I claim my license purchased through Nexcelom Biosciences?
- How can I claim my license purchased through Sysmex-Partec GmbH?
- How can I claim the FCS Express license that came with my Cytek instrument purchase?
- Can FCS Express integrate Python scripts?
- Can I use the FlowAI script in FCS Express?
- Can I use the FlowClean R Script with FCS Express?
- How can I recreate ratiometric data acquired in FACSDiva?
- How do I use R Integration with FCS Express?
- How does FCS Express implement software compensation?
- If my data does not have a Time parameter, can I create one?
- What is compensation?
- What is the compensation workflow in FCS Express?
- Can I customize the display of my data from different instruments?
- Can I disable the live updating feature?
- How can I display all of my detectors for my Cytek data?
- How can I set FCS Express so my FCS 3.0 biexponential data looks the same as it did in the BD FACSDiva software?
- How do I display Summit data in FCS Express as it appears in the Summit Software?
- How do I fix the biexponential axes on a plot?
- How do I rescale CytoFLEX data so it displays as it did at acquisition?
- How do I update my density and contour plots created in Version 4 to use the newest color palette?
- What are resolution options?
- What is Biexponential and Hyperlog Scaling?
- What is the best way to set FCS Express to display FCS 3.0 data from FACSDiva on a 4 decade log scale?
- Where can I get more information regarding DNA analysis using the Multicycle AV?
- Why can’t I change my plot axis labels from the Name keyword to the Stain keyword?
- Why do my dot plots appear sparse and blocky?
- Why is the text on the right most label cut off my plot?
- How are statistics in FCS Express calculated compared to how they are calculated in BD FACSDiva?
- How can I display my statistical data in Scientific Notation?
- What is “Stain Index” and how do I calculate it with FCS Express?
- What is MFI (Mean or Median Fluorescence Intensity) and how do I calculate it in FCS Express?
- Why is the Geometric Mean being reported as NaN or ##ERROR##?
- Are Beckman Coulter LMD files unique?
- Can I find a support resource page for the analysis of Cytek data in FCS Express?
- How can I easily create the "filename" column in the "ExtraKeywordsTable.csv" file?
- How can I load data from the BD Accuri C6 Flow Cytometer?
- How do I change the display in my plots from one data file to another data file?
- How do I export .ICE files from Thermo Cellomics HCS Studio?
- How do I tell FCS Express what plate size to use if that information is not included in the data file?
- How do I upload files to the De Novo Software FTP site?
- How do I use BD Accuri CFlow files with Multicycle DNA analysis in FCS Express?
- What is the Elapsed Time setting in the Gallios software and how do I convert it to real time?
- Why are there sometimes access violations when I save and load files?
- Why do I get the message that a data file exported from a FACSDiva™ Experiment is invalid?
- How do I adjust the axes to display small particle data from Amnis CellStream?
- How do I choose which images and parameters to view in a Data Grid?
- How do I export/save data from IDEAS software and load it in FCS Express?
- How do I make my images in the data grid larger?
- How do I pseudo-color images in a data grid?
- How do I work with Amnis derived image cytometry data in FCS Express?
- Can I display heat maps with my Image Cytometry data?
- Can I work with data from PerkinElmer Instruments?
- Do you offer 21 CFR Part 11 compliance options for the Image Cytometry Version?
- Do you offer image segmentation or image analysis?
- How do I use CellProfiler Data with FCS Express?
- How do I use ImageJ with FCS Express?
- What file formats are compatible with FCS Express Image Cytometry?
- Where can I find Nexcelom Resources and Applications?
FCS Express on Mac
Upgrading FCS Express
- Can different versions of FCS Express exist on the same computer?
- How can I view and convert my V3 layouts to FCS Express 7?
- How do I import my version 3 security databases into newer versions of FCS Express?
- How do I update Density Plots created in Version 4?
- Is there an upgrade discount from earlier versions of FCS Express?
- Why are my density plots from V3 not displayed correctly in later versions?
- Why are there fewer outlier dots on my FCS Express 5 and later density plots than in V4?